BN1719 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 7.5306e-05 1.5157e-04
Layer 4 1.0980e-04 2.1186e-04
Layer 2 1.6736e-04 6.1359e-04
Layer 5 4.1141e-04 4.9870e-04
Layer 6 1.3813e-03 6.3943e-03
WM 9.9898e-01 2.6197e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
DNAJA1 Expression Distribution
Gene Specificity Score (GSS)
DNAJA1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
DNAJA1 Layer 4 4.2129 0.9101
APP Layer 3 4.3633 0.9056
RTN3 Layer 4 4.1797 0.9048
SERINC1 Layer 4 4.4160 0.9039
UBL5 Layer 3 4.3281 0.9033
ATP1B1 Layer 4 4.4414 0.9022
UQCR10 Layer 4 4.5742 0.9018
NDUFS5 Layer 4 4.5078 0.9015
MORF4L1 Layer 4 4.8047 0.9013
GDI1 Layer 3 4.7656 0.9003
COX6B1 Layer 4 4.8789 0.8994
PRNP Layer 2 4.3633 0.8992
SARAF Layer 3 4.2695 0.8987
SRP14 Layer 3 4.3164 0.8986
OAZ1 Layer 4 4.6523 0.8978
BEX3 Layer 3 4.6641 0.8977
COX5B Layer 5 3.9707 0.8976
PRKACB Layer 3 4.9043 0.8974
EIF4G2 Layer 3 4.6680 0.8970
UQCRQ Layer 3 4.1289 0.8968
NTRK2 Layer 3 4.6250 0.8964
NDUFA1 Layer 4 4.8555 0.8963
MTCH1 Layer 5 4.5938 0.8961
COX7A2 Layer 3 4.2539 0.8960
RTN4 Layer 3 3.9707 0.8958
SNX3 Layer 3 4.0410 0.8955
LDHB Layer 3 4.2461 0.8952
NORAD Layer 3 4.6328 0.8950
APBB1 Layer 4 4.6777 0.8949
ACTG1 Layer 4 4.4219 0.8947
NDUFB4 Layer 4 4.7734 0.8945
COX6C Layer 3 4.1562 0.8942
ARPP19 Layer 3 4.3359 0.8941
ENO1 Layer 4 5.2109 0.8941
HSPH1 Layer 4 4.7031 0.8941
EEF2 Layer 4 4.7930 0.8940
COX8A Layer 3 4.7090 0.8938
ITM2C Layer 3 4.6250 0.8935
TSC22D1 Layer 3 4.4766 0.8929
NDUFA3 Layer 3 4.2461 0.8926
CAMK2N1 Layer 2 4.6133 0.8921
MIF Layer 3 4.0742 0.8921
MZT2B Layer 4 4.5742 0.8920
MRFAP1 Layer 4 4.2070 0.8917
PRDX5 Layer 4 5.4258 0.8916
EIF4A2 Layer 4 4.2812 0.8916
ATP6V0B Layer 3 4.4766 0.8907
UQCR11 Layer 3 3.8457 0.8907
BSG Layer 3 4.6523 0.8901
ATP6V0C Layer 3 4.6719 0.8901

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1719
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1719_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1719/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1719/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1719/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1719/report/PD/BN1719_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1719/report/PD/BN1719_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:48:44
  • Number of Processes: 10
  • Spending Time: 0h 3m